7GQ2

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z1954800348


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.1429825% PEG 3350, 0.1M Tris, 0.2M Ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4650.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.698α = 90
b = 62.813β = 90
c = 147.906γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-01-27SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92124DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3562.899.60.0830.0870.0240.99810.411.687945
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3793.22.0932.290.9010.296.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3557.8879393301693.450.190970.190250.20563RANDOM24.26
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.23-0.280.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.709
r_dihedral_angle_3_deg16.348
r_dihedral_angle_4_deg15.943
r_long_range_B_refined10.595
r_long_range_B_other8.113
r_dihedral_angle_1_deg7.345
r_scangle_other5.573
r_scbond_it3.371
r_scbond_other3.37
r_mcangle_other3.226
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.709
r_dihedral_angle_3_deg16.348
r_dihedral_angle_4_deg15.943
r_long_range_B_refined10.595
r_long_range_B_other8.113
r_dihedral_angle_1_deg7.345
r_scangle_other5.573
r_scbond_it3.371
r_scbond_other3.37
r_mcangle_other3.226
r_mcangle_it3.221
r_mcbond_other2.085
r_mcbond_it2.065
r_angle_refined_deg1.698
r_angle_other_deg1.401
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2800
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction